Late graft loss continues to be a major problem after kidney transplantation (KT), mainly as consequence of death with a functioning graft and intrinsic allograft failure (or chronic allograft dysfunction (CAD)). CAD remains a major cause of allograft attrition over time, resulting in reinstitution of end-stage renal disease care. CAD is considered by many to be a variant of chronic kidney disease (CKD), with both immune and non-immune mechanisms, contributing to the development of interstitial fibrosis, tubular atrophy (IFTA) and progressive loss of graft function. Early development of graft fibrosis is predictive of late graft function. To study early factors involved in kidney fibrosis progression, we established a cohort of 298 KT patients followed longitudinally, with sequential genomic sampling of kidney allografts. Paired peripheral samples are also available. Utilizing this unique resource, we have made these observations: a) Molecular activators of early graft injury among KT recipients with kidney allografts progressing to fibrosis are independent of initial cause of injury, b) there is an constant pro-inflammatory and oxidative stress proclivity in the allografts from patients progressing to CRAD, c) specific DNA methylation (DNAm) patterns in donor kidney tissue associate with short- and long-term outcomes post-KT, d) there are major DNAm pattern changes between cross-sectional kidney allograft biopsies with IFTA and decline of graft function and kidney graft biopsies with normal histology and graft function (NFA) at > 2-years post-KT, and e) preliminary data demonstrate that specific upstream epigenetic modifications are associated with canonical gene pathways related to enhanced immune response and impaired allograft reparation. An independent Cohort 2 (multicenter, five Institutions) will be used for validation and replication. Hereby, we hypothesize that regardless of the initial insult after KT, inflammation and oxidative stress induce epigenetic modifications of critical genes, resulting in an increased risk of fibrosis and progressive decline of kidney function. These epigenetic modifications lead to secretion of specific cellular biomarkers into the circulation and urine that predict the risk of kidney fibrosis and chronic allograft dysfunction. The specific aims (SA) include: SA1: Determine post-KT epigenetic modifications sequentially from a longitudinal cohort of human renal allograft biopsies. SA2: Develop predictive models to stratify the risk of developing fibrosis and function loss by integrating the most predictive epigenetic, transcriptome, and clinical markers. SA3: Evaluate circulating small non-coding RNA (sncRNA) profiles to identify biomarkers and correlate with gene expression changes in the renal allograft with fibrosis and CAD. Evaluation of epigenetic changes in kidney grafts may provide new data about affected pathways and regulators leading to graft injury, fibrosis, and loss of function. The proposed studies will provide information about the effect of epigenetic modifications on molecular pathways and upstream regulators leading to CAD. Resulting non-invasive biomarkers will better predict and stratify graft injury and fibrosis progression, potentially improving long-term renal graft outcomes.